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A Knock-Down Cell-Based Study for the Functional Analysis of Chloride Intracellular Channel 1 (CLIC1): Integrated Proteomics and Microarray Study

[ Vol. 28 , Issue. 1 ]

Author(s):

Shang-Jun Yin, Jae-Rin Lee, Bit-Na Lee, Jun-Mo Yang, Guo-Ying Qian, Yong-Doo Park* and Myong-Joon Hahn*   Pages 84 - 100 ( 17 )

Abstract:


Background: Previously, we detected that chloride intracellular channel 1 (CLIC1) was involved in the pathogenesis of atopic dermatitis (AD).

Objective: In this study, we aimed to use high-throughput screening (HTS) approaches to identify critical factors associated with the function of CLIC1 in knock-down cells.

Methods: We down-regulated CLIC1 in human A549 cells via siRNA and then conducted serial HTS studies, including proteomics integrated with a microarray and the implementation of bioinformatics algorithms.

Results: Together, these approaches identified several important proteins and genes associated with the function of CLIC1. These proteins and genes included tumor rejection antigen (gp96) 1, nucleophosmin, annexin I, keratin 1 and 10, FLNA protein, enolase 1, and metalloprotease 1, which were found using two-dimensional electrophoresis (2-DE) proteomics. Separately, NTNG1, SEMA5A, CLEC3A, GRPR, GNGT2, GRM5, GRM7, DNMT3B, CXCR5, CCL11, CD86, IL2, MNDA, TLR5, IL23R, DPP6, DLGAP1, CAT, GSTA1, GSTA2, GSTA5, CYP2E1, ADH1A, ESR1, ARRDC3, A1F1, CCL5, CASP8, DNTT, SQSTM1, PCYT1A, and SLCO4C1 were found using a DNA microarray integrated with PPI mapping.

Conclusion: CCL11 is thought to be a particularly critical gene among the candidate genes detected in this study. By integrating the datasets and utilizing the strengths of HTS, we obtained new insights into the functional role of CLIC1, including the use of CLIC1-associated applications in the treatment of human diseases such as AD.

Keywords:

CLIC1, knock-down, proteomics, microarray, bioinformatics, PPI mappings.

Affiliation:

College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, 315100, Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Genomic Research Center, EBIOGEN Inc., Seoul 07282, Department of Dermatology, Sungkyunkwan University School of Medicine, Samsung Medical Center, Seoul 135-710, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, 315100, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, 315100, Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon



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